The present invention is directed to methods and compositions for detecting pathological conditions. In particular, the invention comprises methods and compositions using biological factors, such as complement components, for detecting pathological conditions.
Diagnostics has traversed a broad range of disciplines from an initial foothold in serologic diagnostics to DNA molecular diagnostics, such as those using PCR. Problems with many current diagnostic technologies include the inability to directly detect species specific mRNA and proteins, and many also lack specificity and sensitivity. The problems of detection of molecular cancer metastasis, detection of residual disease, the early detection of HIV and other viral agents, sensitive carcinogen detection, sensitivity in detection of pathologic proteins or cells in normal tissue, and the need for heightened specificity and sensitivity in the determination of the precancerous state of dysplasia, illustrate the need for more accurate, sensitive and specific assays. Furthermore, most of these assays fail in detection of very low numbers of antigen or analyte targets, such as low number DNA, mRNA, protein or cellular targets in the presence of a large amount of non-specific material such as genomic DNA, mRNA, protein, or cells.
One example of a diagnostic test that has been shown to be inaccurate at a rate higher than wanted is the Papanicolau Cervical Screen (PAP test), developed in 1924 by George N. Papanicolau and Aureli Babes. Koss (1989) reviewed this diagnostic test and concluded that xe2x80x9calthough this cancer detection system (PAP test) has been shown to be effective in reducing the state of morbidity and mortality from invasive cervical cancer in appropriately screened populations, there is no evidence that the PAP test has succeeded anywhere in complete eradication of this theoretically preventable disease.xe2x80x9d The test is based on the theory that pre-cancerous changes still confined to the epithelium of the uterine cervix (carcinoma in situ) could be identified in exfoliative cytologic specimens. On the assumption that the early detection of these pre-cancerous lesions would prevent invasive cancer of the uterine cervix, the test became a widely used test cancer detection and prevention. The test is based upon a labor-intensive complex process, and the outcome depends entirely on human judgment, variable standard at best. What is needed are improvements to the currently used PAP smear.
A major obstacle in an exfoliative cell diagnostic screening test such as the PAP test is the identification, of cells that reflect abnormal cancerous or pre-cancerous changes in the surface epithelium among the multitude of the cells present. Recent FDA regulatory trends have approved the placement of fewer exfoliative cells on the slide to be stained and scored to allow ease of scoring. Paradoxically, this limitation of exfoliative cell numbers results in diminished test sensitivity and false negative results. Currently 30,000 exfoliative cells are scored on a PAP smear. This reduction in cellular sample size decreases the sensitivity of the assay. A better designed diagnostic process would be required to score millions of exfoliative cells with high specificity and sensitivity.
Interpretation of test results possesses a similar dilemma for analysis of cellular smears due to the fact that smears do not always reflect underlying diseases. In the case of invasive cancer, the surface of the lesions is often necrotic and covered by debris resulting in an inability for the smear to reveal obvious cancer cells. The best determinative test involves a careful clinical examination with biopsy of any visual suspicious cervical lesion and additionally, many pre-cancerous and cancerous lesions may be represented in a cellular smear sample by only a few cells with relatively trivial abnormalities. Determination of the presence of dysplasia is also complicated because not all neoplastic cervical lesions shed cells in a uniform fashion and some lesions are difficult to sample.
The principal goal of cervical smear scoring is to not diagnose overt clinical disease, but to detect occult small carcinomas and pre-cancerous abnormalities that may lead to invasive cancer. To achieve this, the diagnostic screen must be sensitive enough to detect low copy number cells of interest, precancerous and occult cancer. The function of the dysplasia screen is to signal the presence of cellular abnormalities and refer the individual for further follow-up. Repeated tests may not result in the same diagnosis and neoplastic conditions may pass undetected. A more valid approach for detection of the presence of dysplasia/neoplasia would be based on multiple factorial assays performed in concert. This includes inspection of the exfoliative sample on the nuclear level, the cell surface level, and the cytoplasmic level to confirm detection of disease.
Other examples of diagnostic assays lacking sensitivity include the HIV assays currently in use. These assays generally do not detect the stage of the disease in the patient because of an inability to detect low copy number targets early in HIV infection. Many of these assays detect seroconversion at approximately 6 months post infection. The assay is based upon one biological response, such as antibody production in response to the virus. A better assay would be one that measured both cellular and molecular biological responses, such as nucleic acid and protein measurements, and detection of cell surface antigens.
Currently, HIV diagnostic tests are configured to identify a large number of viral proteins present in a sample, and the presence of a large-scale antibody produced by the body to the virus. Earlier diagnosis would be invaluable for treatment of the infected persons. Furthermore, DNA diagnostic processes, using PCR, are limited to a small size sample compromises the sensitivity of the diagnostic test. What is needed are improvements in current diagnostic testing for HIV that can detect the infection early in its time-course with a high level of sensitivity that will also permit monitoring of residual disease during therapy of the HIV infected patient.
Other sensitive assays that are needed include those capable of detecting low levels of carcinogens and other harmful compounds, such as Aflatoxin B1 as well as the other polycylic aromatic hydrocarbons (PAHs). Currently, Aflatoxin B1 detection assays are sensitive to a level of parts per billion. This and other carcinogens may form DNA adducts in germ cells as their mechanism of action, and thus even a very few molecules may exert a carcinogenic effect and are undetectable with current tests. Exposure to the Aflatoxin B1 containing material carries increased risk for carcinogenesis in the consumer. What is needed is a diagnostic technology that will possess sensitivity below parts per billion.
Other attempts at measuring infectious agents include the tests for prions. Creutzfeld-Jakob disease (CJD) of humans and bovine spongiform encephalitis (BSE) and scrapie of animals are neurodegenerative diseases caused by prion proteins. The infectious prion is an abnormal disease-producing isoform of the normal prion protein (PrP) called PrPsc. Brain damage in prion disease occurs when abnormal prion protein molecules, as a consequence of ingestion gain entry to the brain and cause normal PrPs to take on the disease causing PrPsc form.
Currently a labeled mouse monoclonal antibody 3F4 has been shown to bind prions with a sensitivity of binding of the antibody of 5 picograms per ml. This indicates that billions of prion protein molecules or greater would be necessary to be present to support detection of binding of the antibody to the aberrant prion. Furthermore, the assay is complex, requiring selective precipitation of PrPsc by sodium phosphotungstate. This inability to more sensitively detect the presence of the prions in TSEs has hampered an understanding of the disease, attempts to determine if a cure scenario is feasible, and development of a vaccine.
What is needed are methods and compositions that will detect the protein in a large sample of plasma and concentrate and collect the normal and the aberrant forms of the prion in a small volume. Furthermore, methods are needed for diagnostic assays that will detect the presence of the aberrant prion protein with high levels of sensitivity.
What is needed are methods and compositions that recognize the presence of very low numbers of infectious or other targets in an excess of non-specific, non-target or normal material. The target may be nucleic acid, such as DNA and RNA, cellular, or protein, in nature. Ideally, these methods and compositions comprise diagnostic technology that supports high levels of specificity and sensitivity in testing procedures. Preferred methods and compositions comprise diagnostic tests that are configured for early detection of the pathologic agent or other target in the sample by examining the DNA, RNA, cell, or soluble protein in solution, to detect the pathologic target earlier in the infection time-course.
The present invention is directed to methods and compositions for detecting pathological conditions. In particular, the invention comprises methods and compositions using biological factors, such as complement components, for detecting pathological conditions. Particularly described are assays for non-specific target elimination that allow for detection of low copy number targets in a large field of nontarget material. Such assays comprise methods comprising CMSA and MACMSA, which preferably comprise detection of complement proteins and components. The assays of the present invention can be used for detection of changes in cellular molecules or nucleic acids that are part of disease states or infections, or can be used for detection of molecules in the environment.
Not only do the methods and compositions of the present invention comprise detection of nucleic acid and other molecular targets, but the methods and compositions of the present invention comprise diagnostics at supramolecular levels to confirm the presence of the pathologic or other cellular targets in tissues. The present invention comprises the analysis of only the cell subset of interest in a very large cell specimen and has the ability to compartmentalize and assay each cell component for the analyte of interest. Other embodiments comprise target analyte sorting and separation from non-specific analyte for increased sensitivity of detection. CMSA comprises the fixation and activation of complement by interactions between cell subset specific surface membrane proteins, and monoclonal or other antibodies. The initiation of the complement fixation process results in the production of the C3a peptide in quantities directly proportional to the extent of complement fixation.
One embodiment of CMSA, called MACMSA, comprises use of a soluble immunogen found in the cytoplasm or released into the cellular environment. These methods and compositions are used to diagnose the presence of pathologic or other specific soluble immunogens in the cytosol or those released into the surrounding media. The diagnostic assays of the present invention are able to accurately diagnose the presence of the disease state and also determine the position of the patient in the time-course of the disease or other process.